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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #22 +/- ##
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+ Coverage 88.40% 90.45% +2.05%
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Files 6 6
Lines 138 241 +103
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+ Hits 122 218 +96
- Misses 16 23 +7
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This test needs to be checked: genomic-features/tests/test_columns.py Line 79 in 45d97ac |
ivirshup
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ivirshup
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Looks good! A few minor things, and one major thing:
Does joining on the protein table work now? That would be great!
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| tables.remove(start_with) | ||
| tables = [start_with] + tables | ||
| print(tables) |
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| print(tables) |
My bad
| print( | ||
| f"Warning: tables {set(tab) - set(self.list_tables())} are not in the database." | ||
| ) |
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Should this be an error?
If it should be a warning, how about warnings.warn instead?
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At the moment it automatically deletes the tables that are not in the database and prints a warning (which I can replace by warnings.warn) unless you think error is preferable
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I think an error makes more sense, since the result is different than what the user asked for.
But we can change that separately.
| assert list(result.columns) == [ | ||
| "gene_id", | ||
| "gene_name", | ||
| "protein_id", | ||
| "gene_biotype", | ||
| ] | ||
| assert ( | ||
| result.loc[result.gene_biotype != "protein_coding", "protein_id"].isna().all() | ||
| ) |
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Yes, this works now. I added the mapping function to ensembldb.py
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Yes, we can close it.
3 participants
Fixes #9 when finished and partly #6 for discoverability of columns